As far as individuals saying "How did it come to this, where one of Nintendo's flagship franchises is selling so low?" I have an opinion.
First, Metroid compared to Mario and Zelda has always sold lower from the first iteration of the series. Here are the numbers according to VGChartz, and I am not using arcade games with Mario and Donkey Kong, but am including one title from SNES:
Mario
Super Mario Bros. (NES) - 40.24 million
Super Mario Bros. 2 (NES) - 7.46 million
Super Mario Bros. 3 (NES) - 17.28 million
Super Mario World (SNES) - 20.61 million
Source: http://www.vgchartz.com/worldtotals.php?name=Mario
Zelda
The Legend of Zelda (NES) - 6.51 million
Zelda 2: The Adventure of Link (NES) - 4.38 million
The Legend of Zelda: A Link to the Past (SNES) - 4.61 million
Source: http://www.vgchartz.com/worldtotals.php?name=Zelda
Metroid
Metroid (NES) - 2.73 million
Metroid 2: The Return of Samus (GB) - 1.76 million
Super Metroid (SNES) - 1.42 million
Source: http://www.vgchartz.com/worldtotals.php?name=Metroid
Conclusions
The Metroid series has been the bottom of Nintendo's barrel when thrown in with Mario and Zelda. The lowest selling console Metroid was Super Metroid. Metroid: Other M's low sales is on par with the history of the series. Fans expecting Other M to sell 5 million has not shown by history in the Metroid series. No single Metroid game (console or otherwise) has ever sold 3 million or more.
Mario and Zelda went through a sophomore slump with Mario 2 and Zelda 2 selling well less than their predecessor, then eclipsed by their successor. Furthermore, new Zelda and Mario games for each new Nintendo console are hard to predict. The sales dropoff from Ocarina of Time to Twilight Princess is the equivalent of driving over a cliff where the Wii version sold in excess of 5 million, the Gamecube version did not sell 2 million, and Ocarina of Time surpassed 7 million. Mario games are just as hard to predict with Super Mario World 2 selling 4.12 million, Super Mario 64 selling 8.55 million, and Super Mario Sunshine selling 6.28 million. Each new Mario and Zelda console game is a crapshoot in Vegas to say the least.
The expectations for Other M are unfounded. If you study up on your Metroid history, your best educated guess or sales prediction should have been at the 1 to 1.5 million mark. Every Metroid game, with the exception of Metroid Prime (considered noncanon by Sakamoto), has followed a pattern of declining sales starting with Metroid 2 on.
The question remains, why were sales predictions drastically higher than expected by the history of the Metroid franchise?